## [1] "test_dataset1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 99,742 99,742
Not Truncated 92,512 92,628
Truncated 7,230 7,114

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 22.4 22.6

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 2,658 2,476
Unique Alignments 3,885 3,725
Multiple Alignments 12,437 12,679
Failed To Align 80,762 80,862
Paired 1,143 1,143

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 401
Invalid Pairs 742
Same Circularised 21
Same Dangling Ends 73
Same Fragment Internal 466
Re Ligation 39
Contiguous Sequence 3
Wrong Size 140
Total Pairs 1,143

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 401 401
Cis-close (<10Kbp) 36 36
Cis-far (>10Kbp) 346 346
Trans 19 19

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics